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Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Joint Genotyping

I ran GATKHaplotypeCaller without GVCF mode. I have got the correct output VCF file. I want to do the joint Genotyping for BSA QTLSeqr analysis. The GATK GenoType is only for gVCF. I cannot run this mode, it takes too much time, even if run the aligner file in intervals. My question, how can I use the joint GenoTyping on the VCF file.


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